Table 1 |
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|
Overrepresented Gene Ontology attributes for genes with 5'UTR introns |
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|
N |
X |
LOD |
P |
P-adj |
Gene Ontology attribute |
|
|
|
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|
25 |
35 |
0.650 |
1.4e-05 |
0.0153 |
GO:0004715: |
non-membrane spanning protein tyrosine kinase activity |
|
27 |
38 |
0.644 |
7.5e-06 |
0.0073 |
GO:0051261: |
protein depolymerization |
|
31 |
44 |
0.633 |
2.1e-06 |
0.0017 |
GO:0051494: |
negative regulation of cytoskeleton organization and biogenesis |
|
32 |
48 |
0.560 |
9.2e-06 |
0.0085 |
GO:0032956: |
regulation of actin cytoskeleton organization and biogenesis |
|
32 |
49 |
0.534 |
1.8e-05 |
0.0193 |
GO:0032970: |
regulation of actin filament-based process |
|
48 |
76 |
0.497 |
6.6e-07 |
0.0004 |
GO:0051493: |
regulation of cytoskeleton organization and biogenesis |
|
39 |
62 |
0.491 |
8.3e-06 |
0.0078 |
GO:0016459: |
myosin complex |
|
43 |
71 |
0.449 |
1.2e-05 |
0.0120 |
GO:0051129: |
negative regulation of cellular component organization and biogenesis |
|
51 |
88 |
0.404 |
1.1e-05 |
0.0114 |
GO:0033043: |
regulation of organelle organization and biogenesis |
|
105 |
216 |
0.243 |
3.5e-05 |
0.0398 |
GO:0015629: |
actin cytoskeleton |
|
1094 |
2356 |
0.232 |
5.7e-33 |
<0.0001 |
GO:0008270: |
zinc ion binding |
|
139 |
294 |
0.220 |
1.3e-05 |
0.0139 |
GO:0003779: |
actin binding |
|
996 |
2218 |
0.199 |
1.4e-23 |
<0.0001 |
GO:0006355: |
regulation of transcription, DNA-dependent |
|
1000 |
2233 |
0.197 |
3.4e-23 |
<0.0001 |
GO:0051252: |
regulation of RNA metabolic process |
|
1061 |
2380 |
0.195 |
7.5e-24 |
<0.0001 |
GO:0045449: |
regulation of transcription |
|
1013 |
2273 |
0.193 |
1.2e-22 |
<0.0001 |
GO:0006351: |
transcription, DNA-dependent |
|
1015 |
2277 |
0.193 |
9.5e-23 |
<0.0001 |
GO:0032774: |
RNA biosynthetic process |
|
191 |
420 |
0.190 |
8.3e-06 |
0.0077 |
GO:0008092: |
cytoskeletal protein binding |
|
1078 |
2436 |
0.189 |
6.6e-23 |
<0.0001 |
GO:0019219: |
regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process |
|
1106 |
2512 |
0.185 |
1.3e-22 |
<0.0001 |
GO:0010468: |
regulation of gene expression |
|
1189 |
2713 |
0.183 |
1.6e-23 |
<0.0001 |
GO:0031323: |
regulation of cellular metabolic process |
|
1088 |
2477 |
0.182 |
8.6e-22 |
<0.0001 |
GO:0006350: |
transcription |
|
1211 |
2791 |
0.175 |
4.7e-22 |
<0.0001 |
GO:0019222: |
regulation of metabolic process |
|
989 |
2267 |
0.174 |
1.2e-18 |
<0.0001 |
GO:0003677: |
DNA binding |
|
1507 |
3515 |
0.172 |
2.9e-25 |
<0.0001 |
GO:0003676: |
nucleic acid binding |
|
1212 |
2825 |
0.165 |
5.5e-20 |
<0.0001 |
GO:0046914: |
transition metal ion binding |
|
1682 |
4053 |
0.147 |
1e-20 |
<0.0001 |
GO:0050794: |
regulation of cellular process |
|
1157 |
2784 |
0.136 |
5.6e-14 |
<0.0001 |
GO:0016070: |
RNA metabolic process |
|
1758 |
4305 |
0.134 |
3.7e-18 |
<0.0001 |
GO:0050789: |
regulation of biological process |
|
1772 |
4364 |
0.129 |
4.2e-17 |
<0.0001 |
GO:0005634: |
nucleus |
|
1463 |
3584 |
0.127 |
1.1e-14 |
<0.0001 |
GO:0006139: |
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process |
|
|
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|
N represents the number of transcripts in the RefSeq collection that have both a 5'UTR
intron and a given GO attribute; X represents the total number of transcripts having that GO attribute. For each attribute,
P is the nominal P-value obtained from a one-tailed Fisher's Exact Test that calculates the probability
that at least N transcripts have the particular attribute given the number of genes with 5'UTR introns.
This nominal P-value is adjusted for multiple hypothesis testing to yield P-adj using a resampling approach that accounts for dependencies among the tested hypotheses
(see [40] for precise procedure). The table is sorted in descending order by the log10 of the odds ratio (LOD score), where |
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|
Cenik et al. Genome Biology 2010 11:R29 doi:10.1186/gb-2010-11-3-r29 |
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and M is the number of all genes, e is a pseudocount of 0.5 and q is the query set size. All attributes with LOD > 0.125 and a P-adj < 0.05 are reported.
